User's Manual molSimplify version 1.0 April, 2016 v1.0 molSimplify Contents 1 General information ................................. 3 1.1 Obtaining molSimplify .............................. 3 1.2 Citing molSimplify ................................ 3 1.3 License ....................................... 3 1.4 Acknowledgments ................................. 4 2 Installation ...................................... 5 2.1 System requirements ............................... 5 2.2 Binaries ...................................... 5 2.2.1 Linux ................................... 5 2.2.2 Mac OSX ................................. 6 2.3 From source .................................... 6 2.3.1 Linux ................................... 6 2.3.2 Mac OSX ................................. 7 2.4 Installed files ................................... 7 2.5 Databases & Post-processing ........................... 8 2.5.1 Chemical database setup ......................... 8 2.5.2 Multiwfn setup .............................. 8 3 GUI overview ..................................... 9 4 Structure generation module ........................... 10 4.1 Building simple structures ............................ 10 4.2 Building more complicated structures ...................... 12 4.3 Force field optimization .............................. 13 4.4 Smart alignment & Force order ......................... 14 4.5 Custom angles ................................... 15 4.6 Building custom structures ............................ 16 4.7 Replacing existing ligands ............................ 17 4.8 Additional molecule placement .......................... 19 5 Random generation module ............................ 21 6 Input files & jobscripts ............................... 23 6.1 Input file generation ............................... 24 6.2 Jobscript generation ............................... 24 7 Similarity search & screening ........................... 26 Page 1 v1.0 molSimplify 8 Post processing .................................... 27 9 Extras ......................................... 29 9.1 Updating the database .............................. 29 9.2 Add geometry ................................... 30 10 Command line options ............................... 31 Page 2 v1.0 molSimplify 1 General information molSimplify is an open source utility that incorporates geometric manipulation routines nec- essary for the generation of transition metal complexes, automated setup and completion of electronic structure calculations, post-processing and data analysis. The software generates a variety of coordination complexes with any number of metals coordinated by ligands in a single or multidentate (chelating) fashion. The code can both build the coordination com- plex starting from a single metal atom or work to functionalize a more complex structure (e.g. a porphyrin or other metal-ligand complex) by including additional ligands or replacing existing ones. molSimplify builds intermolecular complexes for evaluating binding interac- tions and generating candidate reactants and intermediates for catalyst reaction mechanism screening and also supports interaction with chemical databases. Furthermore, it provides a Graphical User Interface (GUI) and is thus accessible to a wider audience since it does not require a lot of prior computational chemistry experience. 1.1 Obtaining molSimplify The binaries, source code and useful documentation can be obtained online by visiting: http://molsimplify.mit.edu. 1.2 Citing molSimplify Any published work that utilizes molSimplify shall include the following reference: - Citation here 1.3 License The software is distributed free of charge under the GPL license: Copyright 2016 Kulik Lab @ MIT molSimplify is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either ver- sion 3 of the License, or (at your option) any later version. molSimplify is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with molSimplify. If not, see http://www.gnu.org/licenses/. Page 3 v1.0 molSimplify 1.4 Acknowledgments This software was developed by Efthymios I. Ioannidis and Heather J. Kulik at the Mas- sachusetts Institute of Technology. The authors would like to especially thank Terry Z. H. Gani for thoroughly testing the code and providing valuable feedback. Page 4 v1.0 molSimplify 2 Installation 2.1 System requirements The binaries and the source code have been tested on 64-bit Ubuntu 14.14 and on 64-bit OSX 10.10.7 and are expected to work on any newer system equipped with Python 2.7 or greater. No particular memory requirements or processor capabilities are needed. 2.2 Binaries Binaries of the program have been compiled for both Ubuntu Linux and OSX. The installa- tion of the binaries depends on the platform and analytical instructions are given below. 2.2.1 Linux For Linux Ubuntu, the only requirement is a working version of Openbabel with the Python bindings (pybel) installed. We suggest installing pybel from source using the following pro- cedure: 1. wget https://sourceforge.net/projects/openbabel/files/openbabel/ 2.3.2/openbabel-2.3.2.tar.gz 2. tar -xvf openbabel-2.3.2.tar.gz 3. mkdir build ; cd build 4. cmake .. -DPYTHON BINDINGS=ON 5. sudo make 6. sudo make install Alternatively pybel can be installed using the standard ubuntu package manager with apt-get install python-openbabel. In both cases, once the installation is complete, open an interactive Python terminal and make sure that import openbabel and import pybel work before running molSim- plify. With pybel installed, the user can download the binary and the supporting files and run the program. The program will guide the user in order to set up a configuration file that is stored under /home/user/.molSimplify in the user's home directory and contains a line that specifies the installation directory (top directory) of the program where all the supporting files are located. The line has the format INSTALLDIR=path. The binary can be moved anywhere, however if the top directory of molSimplify is moved the .molSimplify file will Page 5 v1.0 molSimplify have to be manually updated. The configuration file contains also the paths for files used in database search and post processing analysis (see section 2.5). 2.2.2 Mac OSX For OSX, a package installer has been created that automatically installs the required soft- ware for running the molSimplify app. The user can open the molSimplify.pkg installer, follow the instructions and get molSimplify installed. If the package installer fails, the user can manually install the required packages and then download a copy of the molSimplify app. Two packages are required in order to run the molSimplify app, pybel and imagemagick. The easiest way to install both is to use the brew package manager and issue the following commands on a terminal window: 1. sudo brew install open-babel --with-python 2. sudo brew install imagemagick With pybel installed, the user can download the app, place it under /Applications/molSim- plify.app and run the program. If brew is not installed, install it by running /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" in a terminal window. 2.3 From source In order to install molSimplify from source it is necessary to install openbabel with its Python bindings (pybel) and numpy. Furthermore, additional software is required in order to use the Graphical User Interface (GUI). 2.3.1 Linux To install pybel you can follow the instructions listed in section 2.2.1. To install numpy, you can follow the online instructions or use pip install numpy. In order to enable the GUI, the library PyQt5 with its dependencies needs to be installed first. In order to do that we suggest the following procedure: 1. Download and install Qt5 from source (developer.qt.nokia.com/). 2. Install SIP(http://pyqt.sourceforge.net/Docs/sip4/installation.html) from source. If Python.h is missing use sudo apt-get install python-dev . 3. Install PyQt5 from source (http://downloads.sourceforge.net/project/ pyqt/PyQt5/). Page 6 v1.0 molSimplify Once you have installed PyQt5, open an interactive Python terminal window and check whether import PyQt5 works. If it's successfully installed, you can go ahead and run main.py in molSimplify and set up the required configuration file as explained in section 2.2.1. 2.3.2 Mac OSX In order to run molSimplify from source, we need to install pybel first. We suggest using brew as explained in section 2.2.2 or compiling from source. Then install imagemagick (see section 2.2.2). In order to use the GUI, PyQt5 and its dependencies need to be installed as well. The easiest way is to use the following procedure: 1. Install Qt5 with: sudo brew install qt5 2. Install SIP with: sudo brew install sip 3. Install PyQt5 from source (http://downloads.sourceforge.net/project/ pyqt/PyQt5/) with option --sip-incdir=/usr/local/include 2.4 Installed files With both the binaries or the source code a set of additional files are stored that are required by molSimplify. If you use molSimplify with the molSimplify.app (OSX) these files are stored under /Applications/molSimplify.app/Contents/Resources/, otherwise they are in the installation directory of molSimplify as indicated in the .molSimplify file in the